Does anyone know of a book in the Mobileread Uploads where there is both an epub version and a mobi version, where the epub version shows some of the formatting capabilities of epub v2 that are missing in the mobi version?

Can't think of one off hand. The ePub of Three Men in a Boat in the MR library is a good example of ePub formatting, but the Mobi version there isn't the same illustrated edition. I suppose you could convert that ePub to Mobi and see the difference. I'm assuming you mean old Mobi 7 as the newer KF8 version is very similar to ePub and can do most if not all of what ePub does.